7594507ca126d5242346787e42e13c52ea7709b1
max
  Fri Apr 17 08:40:31 2026 -0700
Add lrSv supertrack: long-read structural variants from 9 studies (hg38).

#Preview2 week - bugs introduced now will need a build patch to fix
Sub-tracks (all bigBed 9+):
han945Sv     - 945 Han Chinese, ONT (Gong 2025, PMID 39929826)
lrSv1kgOnt   - 1019 1000 Genomes, ONT, SVAN-annotated (Schloissnig 2025,
PMID 40702182; lifted from hs1)
tommoJpSv    - 333 Japanese (111 trios), ONT (Otsuki 2022, PMID 36127505)
aou1kSv      - 1027 All of Us, PacBio HiFi (Garimella 2025, PMID 41256123)
ga4kSv       - 502 GA4K pediatric rare disease, PacBio HiFi
(Cohen 2022, PMID 35305867)
decodeSv     - 3622 Icelanders, ONT (Beyter 2021, PMID 33972781)
hgsvc3Sv     - 65 HGSVC3 diverse haplotype-resolved assemblies, HiFi+ONT
(Logsdon 2025, PMID 40702183; merges insdel+inv tables)
kwanhoSv     - 100 post-mortem brains (PD/ILBD/HC), PacBio HiFi
(Kim 2026, PMID 41929179)
chirmade101Sv - 101 long-read WGS GWAS SVatalog cohort
(Chirmade 2026, PMID 41203876)

Includes per-track conversion scripts and autoSql under
scripts/lrSv/, the supertrack summary table in lrSv.html, and a
consolidated makeDoc at doc/hg38/lrSv.txt.

refs #36258

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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+<h2>Description</h2>
+<p>
+This track shows high-confidence structural variants (SVs) identified by
+Oxford Nanopore long-read sequencing of 3,622 Icelanders recruited through
+the deCODE genetics population cohort. The release contains 133,886 SVs
+(55,649 deletions, 75,050 insertions and 3,187 combined insertion/deletion
+events). Variants are site-level (no per-sample genotypes) and have been
+filtered to a high-confidence subset validated in the accompanying
+population-scale analysis.
+</p>
+<p>
+Note that this release does not include allele counts or allele frequencies:
+each row represents a site that was called with high confidence in the
+cohort, but the number of carrier samples is not provided, so the track
+cannot be filtered by AF/AC.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+Items are colored by SV type:
+<ul>
+<li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
+<li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
+<li><span style="color: rgb(140,0,200);">Combined insertion/deletion (INSDEL)</span> - purple</li>
+</ul>
+</p>
+<p>
+Insertions are placed at the insertion site with a width of 1 bp; deletions
+span the deleted interval; INSDEL events span the affected reference region
+and have SVLEN=0 because the reference and alternate alleles differ in both
+sequence and length. Filters are available for SV type and SV length.
+</p>
+<p>
+Where a variant falls inside an annotated tandem-repeat region, the detail
+page also shows the coordinates of that region (TRRBEGIN / TRREND from the
+source VCF), which can be useful context for repeat-mediated insertions and
+deletions.
+</p>
+
+<h2>Methods</h2>
+<p>
+Oxford Nanopore whole-genome sequencing was performed on 3,622 Icelandic
+participants enrolled through deCODE genetics. Reads were aligned to
+GRCh38 and structural variants were called and merged across the cohort
+following the pipeline described in Beyter et al. (2021), which combined
+multiple callers and a joint reassessment of candidate variants against
+the long reads. The high-confidence set released here corresponds to the
+filtered callset with strong read support and consistent representation
+across samples.
+</p>
+
+<h2>Data Access</h2>
+<p>
+The data can be explored interactively in table format with the
+<a href="../cgi-bin/hgTables">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there
+to spreadsheet or tab-sep tables. From scripts, the data can be accessed
+through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>decodeSv</i>.
+</p>
+<p>
+The annotation is stored as a bigBed file that can be downloaded from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our
+download server</a> as <tt>decodeSv.bb</tt>. Individual regions or the whole
+annotation can be obtained with the <tt>bigBedToBed</tt> utility, available
+from our
+<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">utilities
+page</a>. Example:
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/decodeSv.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
+</p>
+<p>
+The original VCF is available from the deCODE genetics
+<a href="https://github.com/DecodeGenetics/LRS_SV_sets" target="_blank">LRS_SV_sets</a>
+GitHub repository.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to the deCODE genetics team and the Icelandic study participants for
+making this dataset publicly available.
+</p>
+
+<h2>References</h2>
+
+
+<p>
+Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA,
+Kristmundsdottir S, Mehringer S, Hardarson MT <em>et al</em>.
+<a href="https://doi.org/10.1038/s41588-021-00865-4" target="_blank">
+Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in
+human diseases and other traits</a>.
+<em>Nat Genet</em>. 2021 Jun;53(6):779-786.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33972781" target="_blank">33972781</a>
+</p>
+